A Myanmar policeman kicks a villager in Kotankauk during a clearance operation in November last year. Evidence of abuse against Rohingya Muslims by the army is growing.
Photograph: Zaw Myo Htike/AFP/Getty Images

More than 1,000 Rohingya Muslims might have been killed in a Myanmar army crackdown, according to two senior United Nations officials dealing with refugees fleeing the violence, suggesting the death toll is far greater than previously reported.

The officials, from two separate UN agencies working in Bangladesh, where nearly 70,000 Rohingya have fled in recent months, said they were concerned the outside world had not fully grasped the severity of the crisis unfolding in Myanmar’s Rakhine state.

“The talk until now has been of hundreds of deaths. This is probably an underestimation – we could be looking at thousands,” said one of the officials, speaking on condition of anonymity. Both officials, in separate interviews, cited the weight of testimony gathered by their agencies from refugees over the past four months in concluding the death toll was likely to have exceeded 1,000.

Myanmar’s presidential spokesman, Zaw Htay, said the latest reports from military commanders were that fewer than 100 people had been killed in a counterinsurgency operation against Rohingya militants who attacked police border posts in October.

Asked about the UN officials’ comments that the dead could number more than 1,000, he said: “Their number is much greater than our figure. We have to check on the ground.”

About 1.1 million Rohingya Muslims live in apartheid-like conditions in north-western Myanmar, where they are denied citizenship. Many in Buddhist-majority Myanmar regard them as illegal immigrants from Bangladesh.

In addition to the information the two UN officials gave Reuters, a report released by the UN Office of the High Commissioner for Human Rights (OHCHR) on Friday gave accounts of mass killings and gang rapes by troops in north-western Myanmar in recent months, which it said probably constituted crimes against humanity.

The government led by Aung San Suu Kyi said last week it would investigate the allegations in the report. It has previously denied almost all accusations of killings, rapes and arson.

But mounting evidence of atrocities by the army puts Suu Kyi, who has no control over the armed forces under a constitution written by the previous military government, in a difficult position, Myanmar-based diplomats say.

The Nobel peace prize winner has been criticised in the west for her silence on the issue, undermining the goodwill she built up as a democracy champion under years of junta rule and threatening international support.

Independent verification of what has been happening in Myanmar is extremely difficult because the military has cut off access to north-western Rakhine.

A second senior UN official, from a different agency in Bangladesh, told Reuters the report described only “the tip of the iceberg”.

The OHCHR report was based on interviews with 220 people, the majority of whom said they knew of people who had been killed or had disappeared.

Reuters also has reviewed a separate, internal UN analysis using a much larger sample size. In this unpublished report, based on interviews with families comprising more than 1,750 refugees, there were 182 reports of killings of people in the interviewee’s home village alone, and 186 reports of people from their village disappearing, accounting for more than 10% in both cases.

The document acknowledges the actual number in both categories was likely lower because interviewees from the same village might have separately described the same incidents.

The UN says 69,000 people have crossed the border since October, so if the proportion reporting people killed or missing among all the refugees was consistent with those in the report the total number would run into the thousands.

The army intensified its offensive in northern Rakhine in mid-November, unleashing what the OHCHR report described as a “calculated policy of terror” after an incident in which several hundred Rohingya attacked an outnumbered group of soldiers, killing an officer.

The OHCHR report details deaths in random attacks, including firing from helicopters and using grenades; targeted killings of imams and teachers, slitting of throats with knives and locking people inside burning houses.

The OHCHR report said the vast majority of the new Rohingya refugees were women and children, raising questions about the fate of the men left behind, UN officials said. “Boys and men between the age of 17 and 45 were particularly targeted, as they are considered to be strong and seen as a potential threat to the army and authorities,” it said, adding that many accounts describe men of that age being rounded up and taken away with their hands tied behind their backs or heads.

Spokesman Zaw Htay said the police and army were doing their jobs in making arrests.

Myanmar authorities have given little information about how many might have been detained, although prison officials told a UN human rights envoy last month they were holding about 450 people. “If you look at the new arrivals – the majority are women – so many of them talk about a killed husband, a slaughtered uncle or a missing brother. Where are all the men?” said the first UN official.